Recent efforts have been directed in developing chips for molecular detection. Of particular interest are DNA chips for sequencing and diagnostic applications. A DNA chip includes an array of chemically-sensitive binding sites having single-stranded DNA probes or like synthetic probes for recognizing respective DNA sequences. A sample of single-stranded DNA is applied to all of the binding sites of the DNA chip. The DNA sample attaches to DNA probes at one or more of the binding sites. The sites at which binding occurs are detected, and one or more molecular structures within the sample are subsequently deduced.
In sequencing applications, a sequence of nucleotide bases within the DNA sample can be determined by detecting which probes have the DNA sample bound thereto. In diagnostic applications, a genomic sample from an individual is screened with respect to a predetermined set of probes to determine if the individual has a disease or a genetic disposition to a disease.
FIG. 1 illustrates a potential hybridization error which can occur with a DNA chip. In this example, a sample DNA molecule 10 falsely hybridizes to a DNA probe 12. The sample DNA molecule 10 includes a first base sequence 14 and a second base sequence 16. The first base sequence 14 is separated from the second base sequence 16 by an intermediate sequence 18. The DNA probe 12 is complementary to both the first base sequence 14 and the second base sequence 16, but is not complementary to the intermediate sequence 18. Such a hybridization error can lead to errors in determining a sequence associated with the sample, or errors in performing a diagnostic using the sample.